Energetics of Nucleic Acid Stability:  The Effect of ΔC_P

Abstract

We report high-resolution differential scanning calorimetric data on the poly(dAdT)poly(dAdT), poly(dA)poly(dT), poly(dIdC)poly(dIdC), poly(dGdC)poly(dGdC), poly(rA)poly(rU), and poly(rI)poly(rC) nucleic acid duplexes. We use these data to evaluate the melting temperatures, TM, enthalpy changes, DeltaHM, and heat capacity changes, DeltaCP, accompanying helix-to-coil transitions of each polymeric duplex studied in this work at different NaCl concentrations. In agreement with previous reports, we have found that DeltaCP exhibits a positive, nonzero value, which, on average, equals 268 +/- 33 J mol(-1) K(-1). With DeltaCP, we have calculated the transition free energies, DeltaG, enthalpies, DeltaH, and entropies, DeltaS, for the duplexes as a function of temperature. Since, DeltaG, DeltaH, and DeltaS all strongly depend on temperature, the thermodynamic comparison between DNA and/or RNA duplexes (that may differ from one another with respect to sequence, composition, conformation, etc.) is physically meaningful only if extrapolated to a common temperature. We have performed such comparative analyses to derive differential thermodynamic parameters of formation of GC versus AT, AU, and IC base pairs as well as B' versus A and B helix conformations. We have proposed some general microscopic interpretations for the observed sequence-specific and conformation-specific thermodynamic differences between the duplexes.

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

“…These investigations were generally performed with either oligonucleotides with several CG pairs at the end 77,84,90,92 or polynucleotides, 103 both of which would massively reduce the impact of fraying. If we set the fraying contribution to zero, we obtain a typical value of −0.06 to −0.07 kcal mol −1 K −1 , in even better agreement with experiment.…”

Heat capacity changes associated with nucleic acid folding

“…Due in part to the limitations of older calorimeters, it has long been assumed that ΔC P s were insignificant for nucleic acid folding, 64,65 although at least one early calorimetric study discussed the possibility of cold denaturation of RNA. 66 Only recently has the occurrence and impact of ΔC P s associated with nucleic acid folding become the focus of systematic investigation (e.g., [67][68][69][70]. Attending the recent influx of ΔC P data for nucleic acid structural changes have been further predictions of the possibility of nucleic acid cold denaturation.…”

Studies of DNA dumbbells VIII. Melting analysis of DNA dumbbells with dinucleotide repeat stem sequences

“…In fact, values of DC p ¼ 64.6 6 21.4 cal/deg-mol have been reported for the DNA melting transition. [40][41][42][43][44][45][46] If DC p = 0, the enthalpy, DH, and entropy, DS, are temperature dependent. The consequence of assuming DC p ¼ 0 is that the transition thermodynamic parameters, DH and DS, evaluated from analysis of the transition region (%60-908C) may be different at temperatures well below the transition region (258C).…”